Sundell David, Mannapperuma Chanaka, Netotea Sergiu, Delhomme Nicolas, Lin Yao-Cheng, Sjödin Andreas, Van de Peer Yves, Jansson Stefan, Hvidsten Torgeir R, Street Nathaniel R
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.
Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden.
New Phytol. 2015 Dec;208(4):1149-56. doi: 10.1111/nph.13557. Epub 2015 Jul 20.
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
对于没有接受过专业生物信息学培训的研究人员来说，访问和探索大规模基因组数据集仍然是一项重大挑战。我们展示了用于探索杨树、针叶树和拟南芥基因组数据的集成平台PlantGenIE.org，该平台包括表达网络和相关的可视化工具。提供了模式生物数据库的标准功能，包括基因组浏览器、基因列表注释、Blast同源性搜索和基因信息页面。通过集成WebApollo支持社区注释更新。我们已经制作了欧洲山杨的RNA测序（RNA-Seq）表达图谱，并将这些数据整合到了表达工具中。还集成了用于进行物种间基因共表达网络保守性比较植物表达分析的ComPlEx资源的更新版本。PlantGenIE.org平台提供了对来自模式林木物种的大规模全基因组学数据的直观访问，既有助于社区对注释改进做出贡献，也有助于支持使用所包含的数据资源来增进生物学见解的工具。
